VMD-L Mailing List

From: Peter C. Lai (pcl_at_uab.edu)
Date: Tue Feb 22 2011 - 12:39:00 CST

In plugins/volutil/Makefile:

line 19:
CXXFLAGS=${CXXFLAGS} -DDEBUG -g -Wall -pedantic

GNU Make 3.81 complains about recursive flags.

http://cesium.hyperfine.info/~cowbert/ports/science/vmd-devel/files/patch-plugins-volutil-Makefile
for the patchfile for this.

On 2011-02-18 11:54:35AM -0600, John Stone wrote:
>
> Hi,
> Thanks for the feedback.
> On linux I'm fairly confident that things should be working well,
> but we're looking for things like the bug the cropped up the other day
> where some files were missing from one of the plugins. So I'd suggest
> that testing the various plugins would be most helpful at this moment.
>
> On Windows and Mac I'm interested in a broader range of feedback,
> particularly including the behavior of the GUI and the installers too.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Feb 18, 2011 at 12:19:38PM -0500, Joseph Bylund wrote:
> > Build went well on "Linux 2.6.35-25-generic #44-Ubuntu SMP x86_64
> > GNU/Linux" and it seems to be running smoothly. Is there anything in
> > specific you want us to test? Thanks for the great program.
> > -Joe
> >
> > On 02/16/2011 12:21 PM, John Stone wrote:
> > >Dear VMD-L,
> > > Here is a preliminary list of the new features and improvements
> > >in the VMD 1.9 beta release I posted yesterday:
> > >
> > >What's new in VMD 1.9?
> > >----------------------
> > > User documentation updates
> > > o Minor improvements and corrections to the VMD User's Guide,
> > > added documentation for new commands and environment variables.
> > >
> > > Performance Improvements
> > > o The "Orbital" representation can now utilize multiple GPUs to
> > > greatly accelerate rendering.
> > > o New CUDA-based multi-GPU radial distribution function calculation,
> > > with the "measure rdf" command.
> > > o Added initial support for OpenCL accelerated molecular orbital
> > > rendering.
> > > o Added initial support for OpenCL accelerated electrostatic potential
> > > calculations for "volmap coulomb".
> > >
> > > General Improvements
> > > o Added "tooltip" mouse-over help and tips to all of the VMD
> > > graphical user interface controls.
> > > o Global label properties are now located in a new tab within
> > > the labels window.
> > >
> > > New rendering and display features
> > > o Updated default representation resolutions for modern era GPUs,
> > > depth cueing is now enabled by default on platforms that support it.
> > > o New and updated stereoscopic display support:
> > > The left and right eyes can now be swapped in any stereo mode,
> > > so the old "Reverse" mode names have now been eliminated.
> > > Anaglyph stereo no longer requires a GPU with support for
> > > quad-buffered stereo.
> > > Added support for column-interleaved and checkerboard stereo modes.
> > > Reorganized stereo controls in the VMD display menu.
> > > o The "display resize" and "display reposition" commands are now
> > > implemented on all platforms.
> > > o Added a new angle-modulated transparency material property that
> > > works similarly to the way Raster3D renders transparent surfaces.
> > > The angle-modulated material property is supported in the
> > > VMD OpenGL Window, and in Raster3D and Tachyon renderings.
> > > o Added new "thickness" controls for atom label text and for
> > > user-defined text drawn using the "graphics" or "draw" commands.
> > > Added code to draw points at font stroke vector endpoints, to
> > > prevent "cracks" from appearing when larger line widths are used.
> > > o VMD atom labels and text are now exported to renderings by
> > > Gelato, Raster3D, POV-Ray, RenderMan, and Tachyon.
> > > o The format of VMD scenes exported to the RenderMan .RIB format
> > > has been updated for the latest versions of PIXAR Photorealistic
> > > RenderMan, and have also been tested with Aqsis, an open source
> > > RenderMan compatible renderer.
> > > o Tachyon renderings now support gradient backgrounds, and have been
> > > updated to more faithfully implement all of the VMD depth cueing
> > > modes.
> > > o Added export of representation group hiearchy and
> > > material properties to Wavefront OBJ files. Wavefront .OBJ files
> > > generated by VMD now take advantage of a more efficient triangle
> > > mesh
> > > storage format that reduces file sizes to half their original size.
> > > Corrected the polygon winding order for spheres and cylinders,
> > > needed for correct two-sided lighting in Maya.
> > > o Increased interactive molecular dynamics force arrow scaling
> > > constant by a factor of 3.
> > >
> > > New and improved analysis commands
> > > o New "measure rdf" command provides fast GPU-accelerated
> > > calculation of radial distribution functions.
> > > o The "volmap coulombmsm" command now supports both periodic
> > > and non-periodic simulation cells (both are also GPU-accelerated).
> > > o New "parallel" commands enable MPI-based compilations of VMD to
> > > perform batch mode parallel analysis jobs on distributed memory
> > > clusters and supercomputers. The "parallel" commands also exist
> > > within non-MPI versions of VMD, so that any analysis script can
> > > be written to automatically adapt to parallel execution.
> > > Parallel collective operations (allgather, allreduce, barrier)
> > > make it possible for parallel analysis jobs to process results
> > > without
> > > using hand-written message passing code and without exchanging data
> > > through the filesystem.
> > >
> > > Other features and improvements
> > > o Enable a much broader range of keycodes in the OpenGL graphics
> > > window,
> > > allowing VMD user-defined hotkeys to be associated with the
> > > 12 function keys, keypad arrows, page-up/down, home, end, insert,
> > > and delete.
> > > o Enable mirror specular reflections for Tachyon renderings when
> > > the environment variable VMDTACHYONMIRRORSPECULAR is set.
> > > Implemented a user-definable threshold for enabling mirror
> > > reflection
> > > in Tachyon renderings when the Phong exponent goes beyond a
> > > specified
> > > limit. The VMDTACHYONPHONGSPECTHRESH variable can be set to
> > > choose a different threshold for enabling mirror reflection.
> > > o Added VMDCUDADEVICEMASK environment variable to give the user
> > > explicit control over the subset of GPUs that VMD is allowed to use.
> > > o Added VMDNOCUDA environment variable to allow the user to prevent
> > > VMD from using GPUs for non-rendering purposes.
> > > o If .vmdsensors file VRPN device names contains @tcp, we enforce
> > > tcp-only connections which can be easily punched through firewalls
> > > and tunneled with ssh.
> > > o Changed the default behavior of X-Windows based VMD builds to
> > > automatically run VMD in text mode if the DISPLAY environment
> > > variable is unset.
> > > o Updated VMD to support Tcl 8.6 API changes.
> > > o Updated VMD to support FLTK 1.1.10
> > > o Updated VMD to support CUDA 3.x, and 4.0
> > >
> > > New and improved plugins and extensions
> > > o autoimd: Added support for the new chirality and cispeptide plugins.
> > > o autoionize: Added ion placement modes to neutralize the system or
> > > set
> > > a salt concentration. Added support for all ions in the CHARMM force
> > > field. Automatically set segname of ions to be placed to avoid
> > > duplicated segments.
> > > o autopsf: correcting the behaviour of "reset autopsf".
> > > o chirality: New plugin for identifying, visualizing, fixing, and
> > > preventing chirality errors in molecular dynamics simulations.
> > > o cispeptide: New plugin for identifying, visualizing, fixing, and
> > > preventing cis peptide bonds in molecular dynamics simulations.
> > > o clonerep: bug fix enabling use of atom selections containing
> > > perl regular expressions.
> > > o colorscalebar: Maintains current views of all molecules when the
> > > scale
> > > bar is added. New GUI option to select molecule and representation
> > > to
> > > use with the autoscale option.
> > > o hbonds: added warning about overlapping selections in measure
> > > hbonds.
> > > o idatm: modified molefacure and runante to be able to run geometry
> > > optimisations using sqm.
> > > o ilstools: Bug fix for package require ordering problem pointed
> > > out by Aaron Oakley.
> > > o mdffplugin: New plugin that implements the Molecular Dynamics
> > > Flexible
> > > Fitting (MDFF) simulation preparation and analysis tools for docking
> > > all-atom structures with Cryo-EM density maps.
> > > o membrane: added the option to build CHARMM36 bilayers.
> > > o molefacture: Update molefacture to use the new ambertools version
> > > of antechamber.
> > > o multiseq: Support for the multiple sequence alignment tool MAFFT
> > > which offers fast multiple alignment methods and can be used
> > > anywhere
> > > within MultiSeq that clustalw is used. The desired title shown
> > > for a sequence can now be changed from simply 'Sequence Name'
> > > to a variety of options including Scientific Name, Common Name,
> > > Domain of Life, and many others.
> > > RMSD and Q calculations work for RNA as well as DNA.
> > > Numerous memory footprint reductions and speed improvements
> > > particularly beneficial for loading large numbers (e.g. 100,000)
> > > of sequences. Lines can now be chosen as a rep type for a given
> > > sequence or for highlighting. MultiSeq can load dot-bracket
> > > notation files for a given sequence and they can be viewed
> > > in the main window.
> > > o namdgui: Fixed menubutton behavior for MacOS X.
> > > o nanotube: Automatically assign bond types and make certain
> > > that bonds are written out. Now uses topotools plugin
> > > instead of writing temporary files. Bug fixes and strict
> > > parameter checking.
> > > o pbctools: New compound options for 'pbc join': fragment, connected.
> > > Alternate joining algorithm based on bondlists. slower, but
> > > can handle arbitrarily long molecules. The 'pbc box' command
> > > now allows the drawing material to be set. Several bug fixes.
> > > o qmtool: Fixed menubutton behavior for MacOS X.
> > > o readcharmmtop: New CHARMM topology for lipids.
> > > o readcharmmpar: New CHARMM topology for lipids.
> > > o rnaview: Now ships with external program RNAView that calculates
> > > base
> > > pairing information from nucleic acid structures (used by the
> > > ssrestraints plugin).
> > > o runante: Scale CM1 charges by 1.14 (Jorgensen's recommendation)
> > > o solvate: Fixed a bug that could lead to incomplete overage of the
> > > solute.
> > > o ssrestraints: Fixed parsing of -hbonds option. Added support for
> > > Amber
> > > RNA residue names.
> > > o symmetrytool: Fixed menubutton behavior for MacOS X.
> > > o timeline: Handles large structures much more efficiently.
> > > o topotools: many bugfixes from version 1.0. Determination of angle,
> > > dihedral and (some) improper definitions (with adjustable tolerance)
> > > from bond topology data. Heuristic determination of atom
> > > properties based on other information (e.g. element from mass,
> > > mass from element, element from name, radius from element, etc).
> > > Support for reading and writing of xmol/xyz style trajectories with
> > > a
> > > varying number of atoms (when bonds are not displayed).
> > > Support for writing synthetic gromacs topology files for
> > > use with gromacs analysis tools for non-gromacs trajectories.
> > > Support for reading data files containing non-orthogonal cells.
> > > Stricter checking for CGCMM extensions to the LAMMPS data file
> > > format.
> > > Encode the intended atom_style setting in data file header.
> > > Parse and compare - if present - against requested atom style on
> > > reading. - write commented out Coeff sections to data files to
> > > provide hints on which coefficients need to be set.
> > > o vdna: Updated with Tom Bishop's latest version.
> > > Fixed uninitialized data preventing the "plot parameters" button
> > > from being used before drawing the DNA.
> > > o viewmaster: Updated handling of material properties for new
> > > features.
> > > o vmdmovie: Added support for both MPEG-1 and MPEG-2 formats using
> > > mencoder. Added support for current ffmpeg 0.5.x encoder on Unix
> > > platforms. Added 4 new FFMPEG encoding targets including MPEG-1,
> > > MPEG-2, and both NTSC and PAL forms of MPEG-2 DVD profiles.
> > > Fixed ppmtompeg frame counters to handle movie sequences with
> > > up to 100000 frames.
> > > o volutil: New plugin for processing Cryo-EM volumetric density map
> > > files,
> > > used by the MDFF plugin.
> > >
> > > New and improved file import and export
> > > o Abinit plugin: Added Rob Lahaye's VMD plugin for reading ABINIT
> > > files.
> > > o CHARMM COR plugin: prevent uninitialized variables on some
> > > platforms.
> > > o DCD plugin: Detect and works around bugs in DCD files written by
> > > older versions of Vega ZZ which generated incorrectly formatted
> > > DCD trajectories.
> > > o DTR plugin: Misc bug fixes provided by DESRES.
> > > o HOOMD plugin: Added support for new acceleration field.
> > > o LAMMPS plugin: allow remapping of fields via an environment
> > > variable.
> > > Added read support for triclinic simulation cells.
> > > Improved precision of PBC box angle computation.
> > > Improved support for reading of atoms sorted by their atom id.
> > > Added support for writing trajectory files of non-orthogonal cells.
> > > o MAEFF plugin: Latest version of Maestro plugin from DESRES.
> > > This version adds support for Smiles strings.
> > > o MDF plugin: handle MDF files containing more than 9 molecules, catch
> > > and gracefully handle any problems with bond parsing.
> > > o Molden plugin: Fixed memory leak, and improved documentation.
> > > Enable splitting SP-shells into one S- and one P-shell.
> > > o PSF plugin: Added preliminary parsing of CHARMM PSF files
> > > constructed
> > > for the Drude polarizable forcefield. Gracefully handle PSF files
> > > that contain missing or incorrect bond information.
> > > o PQR plugin: now handles HETATM records correctly, and gracefully
> > > handles
> > > some varations in file structure
> > >
> > > Bug Fixes
> > > o The Python global interpreter lock (GIL) is held when callbacks
> > > are invoked to prevent problems with Tk events come in.
> > > o Fixed incorrect material property tags for Python materials
> > > interface.
> > > o Fixed a potential memory corruption problem in "within" selections
> > > on systems with fewer atoms than CPU cores.
> > > o Fixed the polygon winding order for two-radius cones for polygonal
> > > renderers.
> > > o Updated atom picking logic to take into account clipping of
> > > displayed geometry (and thus associated pick points) against both
> > > the view frustum and the active set of user-defined clipping planes.
> > > o Fixed a case where wireframe Surf renderings were
> > > leaving the linestyle and line width unspecified.
> > > o Catch NULL pointers, which can (very rarely) be returned by
> > > OpenGL drivers if certain types of catastrophic errors occur.
> > > o Fix memory leak when defining angles, dihedrals and impropers via '
> > > molinfo set angles'.
> > > o Excluded old Cygwin-based builds of the "intersurf" plugin
> > > that encounter problems with recent Cygwin installations.
> > >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
===============================================================
Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl_at_uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |
===============================================================